R Markdown

This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see http://rmarkdown.rstudio.com.

When you click the Knit button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:

setwd('/Users/zhassulan_zhaniyazov/Desktop/trgn510/mygraph2/bin') 
mygenes <- read.csv('gene_dist_head.tsv', header= TRUE, sep = "\t", fill = TRUE) 
autosomes <- c("1","2","3","4","5","6","7","8","9","10",
             "11","12","13","14","15","16","17","18","19","20","21","22")  
genes <- mygenes[which(mygenes$chr %in% autosomes),] 
genes$chr <- factor(genes$chr, levels = autosomes)

Including Plots

You can also embed plots, for example:

library(ggplot2)
ggplot(data = genes) +
 geom_bar(mapping = aes(x = chr, fill = feature), width = 1) +
 coord_polar()

library(plotly)
## 
## Attaching package: 'plotly'
## The following object is masked from 'package:ggplot2':
## 
##     last_plot
## The following object is masked from 'package:stats':
## 
##     filter
## The following object is masked from 'package:graphics':
## 
##     layout
p <- ggplot(data = genes) + 
 geom_bar(mapping = aes(x = chr, fill = feature), width = 1) 
 ggplotly(p)

Note that the echo = FALSE parameter was added to the code chunk to prevent printing of the R code that generated the plot.